Research workbench
Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with hmbpp
Analyse Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6J0G
- Type
- protein
- Length
- 758 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Butyrophilin subfamily 3 member A3
- UniProt
- O00478
- Ligands
- H6P
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Butyrophilin subfamily 3 member A3 | protein | 190 | 7% helix, 36% strand | O00478 |
| C, D | Butyrophilin subfamily 3 member A3 | protein | 189 | 6% helix, 37% strand | O00478 |
Ligands and binding sites
- H6P · (2E)-4-hydroxy-3-methylbut-2-en-1-yl trihydrogen diphosphate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1100 | 0.76 | 0.78 | 115 | H6P |
| 2 | 97 | 0.42 | 0.77 | 17 | H6P |
| 3 | 64 | 0.42 | 0.81 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–D · 663 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 662 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 142 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 98 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 65 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6J0G · Crystal structure of intracellular B30.2 domain of BTN3A3 mutant in complex with HMBPP · the same entry in another collection · chain D against D, TM-score 1.00
- O00478 · AlphaFold monomer V2.0 prediction for butyrophilin subfamily 3 member A3 (O00478) · a predicted model of the same protein · chain B against A, TM-score 0.98
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt O00478
- Elsewhere: RCSB PDB 6J0G · PDBe 6J0G · UniProt O00478
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